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MajorEvan Lorne reports back from M4D-058 and tells them they encountered a race of humans who has Dr.Rodney McKay's face on their flag. They learn that a game McKay and Lt. ColonelJohn Sheppard were playing is actually happening in reality. However, this also causes friction between McKay and Sheppard's worlds, who are on the brink of war.

For two years, Lt. ColonelJohn Sheppard and Dr.Rodney McKay have been playing a computer game left by the Ancients, in which they each develop countries on opposite sides of a river in competition with one another. While McKay has been pushing his country ("Geldar", named after a former romantic interest of McKay's) to develop technologically, Sheppard has been encouraging his ("Hallona", named by the Ancients who created it) to develop its military.

On a routine survey mission, however, MajorEvan Lorne's team discovers that it is not, in fact, a game. Their countries, and all the people in them, are real; living on a planet somewhere in the PegasusGalaxy. With a satellite network in orbit to track their development and Ancient technology to receive the "players'" instructions, their civilization has, in fact, been a Lantean social experiment. The team has stumbled upon McKay's country (easily identifiable by the multitude of paintings of his face throughout the village), they go to the planet to investigate.

Oracle console.

The team visits Geldar first, where they are met by Nola; she immediately recognizes McKay as their "Oracle", and explains that their people were given life thousands of years ago and guided by the Oracle through a console, but then all communications suddenly ceased — interrupted by the war with the Wraith. Unknowingly, McKay and Sheppard have picked up where they left off.

While McKay stays with Nola, Sheppard takes Teyla Emmagan and Ronon Dex to visit "his" civilization, located across the river. There they meet Baden, the aggressive leader of Hallona. He reveals that at the command of Geldar's Oracle, the Geldarans have begun mining for valuable coal under his country. He believes that the proper response is to launch an attack.

Oracle Console up close

The two leaders are brought back to Atlantis to learn about the Ancient technology and to have their dispute mediated by Dr.Elizabeth Weir, but they refuse to cooperate. Tensions are high, and as a result of Sheppard and McKay's "game", the two peoples now stand on the brink of war. Despite their best attempts, neither Weir, McKay, nor Sheppard can convince them to make peace, and things quickly escalate into an all-out attack.

Baden's Oracle console.

On both sides, it soon seems as if the other side has achieved total victory. Geldar is seemingly overrun by the larger Hallonan army and its people slaughtered, while Hallona seems to have been devastated by Geldaran bombing runs (completed by use of dirigibles). After both sides admit defeat, McKay and Sheppard reveal to their respective countries that the whole display was a ruse in order to show them how costly a war could be. The Daedalus, having arrived earlier in expectation of the conflict, was transmitting fake data to each control console while using precision attacks to simulate the damage outside. It seems as though a peace has been achieved, and both civilizations set out on their own, no longer constrained by the game - which has now been deactivated and sealed at Weir's command. After which McKay says that he and Sheppard will stick to chess from now on.

McKay: Let me ask you a question. Say there is a runaway train. It's hurtling out of control towards ten people standing in the middle of the tracks. The only way to save those people is to flip a switch and send the train down another set of tracks. The only problem is... there is a baby in the middle of those tracks.Teyla: Why would anyone leave a baby in harm's way like that?McKay: Well, I don't know. It's not the point. It's an ethical dilemma. Look, Katie Brown brought it up over dinner the other night. The question is: Is it appropriate to divert the train and kill the one baby to save the ten people?Ronon: Wouldn't the people just see the train coming and move?McKay: No, no, they wouldn't see it.Ronon: Why not?McKay: Well... Look... I don't know. Say they're blind.Teyla: All of them?McKay: Yes, all of them.Ronon: Then why don't you just call out and tell them to move out of the way?McKay: It's because they can't hear you.Sheppard: What, they're deaf too? How fast is the train going?McKay: But the speed doesn't matter!Sheppard: Well, sure it does, if it's going slow enough you could out run it and shove everyone to the side.Ronon: Or better yet, go get the baby.McKay: For God's sake, I was just--

Sheppard: The first thing Rodney did after naming his country was stick his face on the flag.

Nola: You sent crates of citrus fruit! Citrus! Do you have any idea what an insult that is to my people?Baden: Didn't used to be.Weir: Okay, see, I think I know where that comes from. Did the Oracle tell you that citrus fruit was bad?Nola: He made us aware of its toxic properties, yes.

Lorne: What are you talking about! It's a perfectly reasonable request!Zelenka: Yeah, perfectly reasonable. I give you all of my food and my people starve.Lorne: I'm not asking you to give me all your food! Plus I did say we would make a deal.Zelenka: Oh yeah, baskets!Lorne: Big baskets! Two dozen of them, hand woven and very nice.Zelenka: Very nice? What am I going to put in them? Huh? Certainly not food!Lorne: You know what? I think you're holding out on me. I think you have plenty of food!Zelenka: Are you calling me a liar!?Lorne: No, I think you're trying to squeeze me for a better deal, that's what I think.Zelenka: Oh! I've got nothing to hide!Lorne: OK! OK! We'll send some of our army troops down and we'll have a look!Weir: What the hell are you two doing!?... I thought I gave specific orders to stay away from this device?Zelenka: Yes, yes you did.Lorne: We just saw that there were some people in trouble and we thought that maybe we could, ah, help.Weir: No! No more help, clearly we are not qualified. Now turn this thing off, disconnect the power and seal the room.Zelenka: Yeah, but, OK...Weir: Now!Zelenka: Mmm... yes ma'am.

McKay: Yeah, don't worry we're gonna stick to chess from now on.Sheppard: As long as Rodney doesn't cheat.McKay: Oh please, like I need to cheat playing you.Weir: OK, I'll leave you to it then.McKay: Ha!Sheppard: Ha! Check Mate.McKay: What? Oh, no, no, no, no, no. What happened there?Sheppard: What happened there is I just kicked your ass.McKay: No, no, I was distracted. She was, uh...OK were going again. Best of ten.

There is a side plot where Dr.Radek Zelenka and MajorEvan Lorne play the "game" with a different planet that ends in the two arguing and being told to stop by Dr.Elizabeth Weir. This was added after the completion of the episode as it was short.

While talking about when Sheppard and McKay started playing "The Game", it is stated that Sheppard's civilization sent McKay's civilization many crates full of citrus as a gift. McKay believes he is deathly allergic to citrus. McKay had taught his civilization that citrus was toxic even though they had eaten it for thousands of years before the Oracle returned. This is apparently what started hostilities between the two nations.

McKay tries to start a discussion about the Trolley Problem in the opening sequence, but the other members of his team refuse to play by the rules of the hypothetical.

In the flashback sequence, while McKay is explaining the customizable "characters" in a voice-over, he is shown fabricating a character that very closely resembles Lt. ColonelSamantha Carter. Nola, the leader of Geldar, also has short blonde hair and blue eyes.

The Geldar flag appears to be based on the national flag of Canada - McKay's home country - with McKay's head replacing the red maple leaf.